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TNT-Tree Analysis using New Technology
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Harriet Nuttall
, …
Martín Morales
6
Sep 5
Problems applying hard constraint tree to a fossil maximum likelihood tree
Hi. Apparently you have a problem with the TNT installer. I suggest manual installation. There is a
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Problems applying hard constraint tree to a fossil maximum likelihood tree
Hi. Apparently you have a problem with the TNT installer. I suggest manual installation. There is a
Sep 5
Jacqueline Silviria
Aug 11
Errors with EIW assuming xlinks
Out of curiosity, I tried running a default NT search with almost all boxes checked for Puschel et al
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Errors with EIW assuming xlinks
Out of curiosity, I tried running a default NT search with almost all boxes checked for Puschel et al
Aug 11
Dalton Meyer
, …
Apirut Nilpanapan
3
Jul 17
TNT 1.6 Maxiumum RAM
Hello Dalton, I used to have this issue (32 Gb of RAM PC). In the TNT 1.6 Windows edition, the “mxram
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TNT 1.6 Maxiumum RAM
Hello Dalton, I used to have this issue (32 Gb of RAM PC). In the TNT 1.6 Windows edition, the “mxram
Jul 17
Daniel Nakamura
,
Edward SIddall
2
Jun 15
How to compare trees using Cluster Information Dist
This may be entirely how you saved the trees. On Jun 3, 2025, at 7:45 PM, 'Daniel Nakamura'
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How to compare trees using Cluster Information Dist
This may be entirely how you saved the trees. On Jun 3, 2025, at 7:45 PM, 'Daniel Nakamura'
Jun 15
Guoyi Zhang
, …
Serdar Sönmez
4
May 29
guoyi.run: One-step TNT script for maximum parsimony phylogenetic
Hello Guoyi, Thank you very much for sharing the script and the paper Best Jonathan Liria <
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guoyi.run: One-step TNT script for maximum parsimony phylogenetic
Hello Guoyi, Thank you very much for sharing the script and the paper Best Jonathan Liria <
May 29
Serdar Sönmez
May 29
Handling Polymorphic States with Asymmetric Stepmatrix in TNT (Windows Interface)
Hello everyone, I am currently facing a challenge in TNT regarding the treatment of polymorphic
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Handling Polymorphic States with Asymmetric Stepmatrix in TNT (Windows Interface)
Hello everyone, I am currently facing a challenge in TNT regarding the treatment of polymorphic
May 29
Daniel Nakamura
, …
asher...@gmail.com
5
Apr 13
Using ttags to save bootstrap and branch lengths in the same newick file
Thanks Martin! It works. FYI others should remember to delete in "phylogram.tree" the first
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Using ttags to save bootstrap and branch lengths in the same newick file
Thanks Martin! It works. FYI others should remember to delete in "phylogram.tree" the first
Apr 13
Adam Cossette
Mar 20
Command line newbie
All, I use a windows machine and click my way through commands in TNT. Yesterday after doing that for
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Command line newbie
All, I use a windows machine and click my way through commands in TNT. Yesterday after doing that for
Mar 20
lv xiao
Mar 5
Question on negative Bremer support value and synapomorphies
Dear all, I have been learning TNT recently based on a toy dataset of 55 taxa each with 50 continuous
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Question on negative Bremer support value and synapomorphies
Dear all, I have been learning TNT recently based on a toy dataset of 55 taxa each with 50 continuous
Mar 5
ENRIQUE TORRES PARISH
, …
Edward SIddall
6
Feb 20
Problems calculating the CI and RI index
You can always do this yourself character by character. Minsteps = number of states. Maxsteps is
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Problems calculating the CI and RI index
You can always do this yourself character by character. Minsteps = number of states. Maxsteps is
Feb 20
Geraldo Alonso Góes Rocha
,
Ambrosio Torres Galvis
3
Jan 2
Suggested commands for huge 244 taxa/126 characters matrix
Dear Geraldo, the routine you are using seems unnecessarily heavy. One of the main reasons TNT is
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Suggested commands for huge 244 taxa/126 characters matrix
Dear Geraldo, the routine you are using seems unnecessarily heavy. One of the main reasons TNT is
Jan 2
Muawiz Chaudhary
,
Santiago Catalano
3
12/20/24
Resistant Fit Alignment
Thanks Santiago, this was very helpful and solves my question. I'll update this thread if my
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Resistant Fit Alignment
Thanks Santiago, this was very helpful and solves my question. I'll update this thread if my
12/20/24
อภิรัตน์ นิลพนาพรรณ
11/19/24
Bremer.run error in TNT v1.6 (Windows11)
Dear erveyine I am using TNT 1.6 on Windows 11, and when I try to use the command 'Bremer'
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Bremer.run error in TNT v1.6 (Windows11)
Dear erveyine I am using TNT 1.6 on Windows 11, and when I try to use the command 'Bremer'
11/19/24
T. Xu
,
Mark
2
11/4/24
TBR branch-swapping with 1000000 trees found (overflow)
The “hold" you are using inside of xmult is not the same as the global “hold”. So, presumably
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TBR branch-swapping with 1000000 trees found (overflow)
The “hold" you are using inside of xmult is not the same as the global “hold”. So, presumably
11/4/24
Kajal Chandra
9/30/24
Help to load input files in TNT
Hello, I am for the first time with TNT, I am interested in generating Bremer support and mapping
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Help to load input files in TNT
Hello, I am for the first time with TNT, I am interested in generating Bremer support and mapping
9/30/24
Buz Wilson
8/12/24
xlinks allowed combinations
Dear TNT folk I have sent this message as a bug report but perhaps someone else out there could
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xlinks allowed combinations
Dear TNT folk I have sent this message as a bug report but perhaps someone else out there could
8/12/24
Adam Cossette
, …
Mark
4
8/12/24
Issues when searching trees from ram
One of the powers of the new technology search, over the traditional search is that in the
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Issues when searching trees from ram
One of the powers of the new technology search, over the traditional search is that in the
8/12/24
Adam Cossette
,
Mark
2
8/9/24
Confusion when searching trees from RAM
When some replicates overflowed it generally means that while you may have run 1000 replicates, some
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Confusion when searching trees from RAM
When some replicates overflowed it generally means that while you may have run 1000 replicates, some
8/9/24
Carolina H-Sepúlveda
7/23/24
Re: Implied weighting on certain species
Hi dear Tao, I hope everything is fine, I'm very grateful to receive your email. Thanks a lot!
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Re: Implied weighting on certain species
Hi dear Tao, I hope everything is fine, I'm very grateful to receive your email. Thanks a lot!
7/23/24
Shawn DeNarie
, …
Nick Matzke
5
7/16/24
Exporting and Opening Trees with Node Supports and Bremer Supports in Nexus Format
Hi all, It may well depend on your specific method for exporting tags in TNT, but I wrote some
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Exporting and Opening Trees with Node Supports and Bremer Supports in Nexus Format
Hi all, It may well depend on your specific method for exporting tags in TNT, but I wrote some
7/16/24
ZQ Xu
4/23/24
Doubts about the use of the script wincladtree.run
Hi TNTers. I'm having some problems with the TNT display tree file call wincladtree.run, I can
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Doubts about the use of the script wincladtree.run
Hi TNTers. I'm having some problems with the TNT display tree file call wincladtree.run, I can
4/23/24
ZQ Xu
4/23/24
Seeking help with analyzing combinations of multiple data types
Hi TNTers. Has anyone combined multiple data (eg coding data, molecular data, geometric morphology
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Seeking help with analyzing combinations of multiple data types
Hi TNTers. Has anyone combined multiple data (eg coding data, molecular data, geometric morphology
4/23/24
T. Xu
, …
Martín Ramírez
5
4/22/24
weird consensus tree
Hi Tao, It is probably because you have taxa without any data in common, eg, Palaemon_concinnus
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weird consensus tree
Hi Tao, It is probably because you have taxa without any data in common, eg, Palaemon_concinnus
4/22/24
Jacqueline Silviria
,
Santiago Catalano
3
4/17/24
[TNT] Colleague having problems saving node labels/tree tags to NEXUS format
Hi Jacqueline, have you solved the issue of exporting the tree labeled? bests Santi On Fri, Apr 12,
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[TNT] Colleague having problems saving node labels/tree tags to NEXUS format
Hi Jacqueline, have you solved the issue of exporting the tree labeled? bests Santi On Fri, Apr 12,
4/17/24
Rob Hun
2
3/26/24
Gaps at the beginning of a nucleotide sequence are treated differently?
This was solved by a very thorough and quick response from Pablo (TNT's bug reporting). In case
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Gaps at the beginning of a nucleotide sequence are treated differently?
This was solved by a very thorough and quick response from Pablo (TNT's bug reporting). In case
3/26/24
antoine laboury
3/12/24
TNT V1.6 on mac M1 freezes when using Xmult
Dear everyone, I am using TNT command version V1.6 on a mac M1 for a couple of years now. However,
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TNT V1.6 on mac M1 freezes when using Xmult
Dear everyone, I am using TNT command version V1.6 on a mac M1 for a couple of years now. However,
3/12/24
Alex Maile
,
Martín Morales
3
2/5/24
Error in running GUI
Hello again, Another user reported the same issue and it's not a problem of architecture. As a
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Error in running GUI
Hello again, Another user reported the same issue and it's not a problem of architecture. As a
2/5/24
Rutger Vos
, …
pierre gousset
6
2/5/24
still confused about constraints
Dear Pablo, Thank you for your answer. In fact, I found the solution to my issues, mainly thanks to a
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still confused about constraints
Dear Pablo, Thank you for your answer. In fact, I found the solution to my issues, mainly thanks to a
2/5/24
M Lee (Zeke)
12/4/23
How to match morphological results with molecular?
Hello everyone, I'm Zeke. I use TNT version 1.5 for phylogenetic analysis based on morphological
unread,
How to match morphological results with molecular?
Hello everyone, I'm Zeke. I use TNT version 1.5 for phylogenetic analysis based on morphological
12/4/23
Tariq
,
Martín Morales
2
12/1/23
Download link broken?
Hello Tariq. I'm not sure if this is your case but the site is experiencing a https problem. A
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Download link broken?
Hello Tariq. I'm not sure if this is your case but the site is experiencing a https problem. A
12/1/23